US9512449B2

US9512449B2 - Method for producing phenol from renewable resources by fermentation

Info

Publication number: US9512449B2
Application number: US14/442,468
Authority: US
Inventors: Jorgen Magnus
Original assignee: Covestro Deutschland AG
Current assignee: Covestro Deutschland AG
Priority date: 2012-11-13
Filing date: 2013-11-13
Publication date: 2016-12-06
Anticipated expiration: 2033-11-13
Also published as: EP2920302A1; WO2014076113A1; US20160273005A1; BR112015010557A2; CN104995298A; CA2890922A1

Abstract

The invention relates to a method of generating a recombinant host strain for producing phenol, comprising the steps of a) providing a host comprising chorismate, b) transforming the host with a first nucleic acid sequence comprising ubiC (SEQ ID NO: 1) encoding chorismate lyase that converts chorismate to 4-hydroxybenzoate, and c) transforming the host with a second nucleic acid sequence encoding an oxygen-tolerant 4-hydroxybenzoate decarboxylase that converts 4-hydroxybenzoate to phenol, thereby generating a recombinant host that is capable of producing phenol under aerobic conditions, wherein step b) and step c) are carried out simultaneously or sequentially. The invention also provides the recombinant host strain for producing phenol obtainable by the aforementioned method, as well as a method of producing phenol in the recombinant host strain.

Description

This application is a 371 of International Patent Application No. PCT/EP2013/073688, filed Nov. 13, 2013, which claims foreign priority benefit under 35 U.S.C. §119 of European Patent Application No. 12192342.9, filed Nov. 13, 2012, the disclosures of which patent applications are incorporated herein by reference.

TECHNICAL FIELD

The invention relates to the field of producing phenol from renewable sources, such as e.g. biomass in a suitable recombinant host.

INTRODUCTION

Phenol is currently produced at several million tonnes per year from fossil raw materials, predominantly by the cumene process, i.e. a chemical process. Such fossil raw materials are not renewable as opposed to raw materials which are renewable, such as the renewable resource “biomass”. A production process based on renewable resources, such as biomass, would achieve independence from fossil resources and would have the potential of saving large amounts of CO₂emissions.

Phenol is a chemical intermediate used in industry in the production of phenolic resins, bisphenol A caprolactame and other chemicals. Phenol that is based on renewable resources, which is referred to here in the context of the invention as “biophenol”, is strongly desired in order to reduce production cost and become independent of fossil resources. More importantly, chemical companies have committed themselves to reduce CO₂emissions both for their own processes as well as by increasing the use of renewable resources in their raw materials. Biophenol has a high potential of avoiding fossil resources and saving CO₂emissions, accordingly.

The production of chorismate in bacteria was described in Sprenger G A, “From scratch to value: engineering Escherichia coli wild type cells to the production of L-phenylalanine and other fine chemicals derived from chorismate”, Appl Microbiol Biotechnol 2007, 75:739-749.

The production of phenol in bacteria has been described by Wierckx N J P et al., “Engineering of solvent-tolerant Pseudomonas putida S12 for bioproduction of phenol from glucose”, Appl Environ. Microbiol. 2005. 71:8221-8227.

However, the biosynthesis pathway used by Wierckx et. al first builds up the molecule tyrosine from chorismate by incorporating an amino group from glutamate, and then breaks it down to phenol releasing the amino group again. This pathway comprises more reaction steps, and is energetically less favouorable than the method according to the invention due to the longer pathway which leads to the deamination of glutamate. Using tyrosine as an intermediate for the biosynthesis of phenol is also a disadvantage because tyrosine is a strong inhibitor of the activity of the genes in the aromatic amino acid pathway. The inhibition takes place at genome level (gene repression), transcriptome level and metabolome level (feedback inhibition). In contrast, the method according to the invention converts chorismate directly to phenol, as described below, which is less complex, energetically more efficient and has a higher potential of yielding high production rates of phenol.

In addition to the above pathway over tyrosine to produce phenol in bacteria, it is also known that phenol can be produced by chemical conversion of shikimic acid, wherein the shikimic acid is produced by fermentation (Gibson J M et al., Benzene-Free Synthesis of Phenol, Angew. Chem. 2001 113(10):1999-2002).

The biosynthesis of 4-hydroxybenzoate over tyrosine was also reported. Meinen et al. used the biosynthesis pathway over tyrosine (Meijnen J P et al., Improved p-hydroxybenzoate production by engineered Pseudomonas putida S12 by using a mixed-substrate feeding strategy. Appl Microbiol Biotechnol. 2011. 90(3):885-93.).

WO2012063862 describes a method for producing phenol by fermentation. The pathway over chorismate and 4-hydroxybenzoate was used by introducing the genes for a chorismate-pyruvate lyase and a 4-hydroxybenzoate decarboxylase in a Corynebacterium glutamicum strain. However, phenol is toxic for Corynebacterium glutamicum and this strain stops to grow at low concentrations of phenol. The growth phase and the production phase are therefore separated in a two-step process, wherein the second step is performed in a different medium than the first and the redox potential is lowered to −450 mV. Combined growth and production using only one fermentation vessel is not possible according to the invention reported in WO2012063862. For the same reason it is not possible to run a continuous fermentation with in-situ product removal where the biomass is regenerating itself by growth.

DEFINITIONS

The term “host” within the meaning of the invention can comprise any host that is capable of producing chorismate, either naturally, only after transformation, or in addition to the naturally present chorismate following transformation. A “host” according to the invention can be selected from the group consisting of bacteria, yeast and fungi.

The term “genetic modification” within the meaning of the invention can comprise deletions as well as transformations. For example, a genetic modification can be a deletion or a transformation that causes the host to overproduce chorismate. Such overproduction of chorismate in the host can be achieved by introducing one or more genetic modifications in the host. Accordingly, the host can comprise one or more genetic modifications to overproduce chorismate. These genetic modifications can have the effect that the host is producing chorismate at levels that are elevated, above the normal, endogenous physiological levels that are present in the host by nature.

The term “transformation” within the meaning of the invention comprises plasmid transformation as well as chromosomal transformation. In plasmid transformation the transformed DNA is uncut and circular and therefore is held extrachromosomally in the host. In chromosomal transformation the transformed DNA is cut and therefore linear and can thus be integrated into the chromosomal genome of the host to be transformed. Essentially, for chromosomal transformation, the host can be transformed with a short piece of linear DNA that can be integrated into the chromosomal genome of the host to be transformed.

The term “in-situ product recovery” within the meaning of the invention refers to the removal of phenol directly from the fermentation broth by using a suitable technique, while the fermenter broth is continued to be used in the fermentation. This may include circulating the fermentation broth through an external apparatus where the phenol is removed from the fermentation broth before the fermentation broth is partly recycled to the fermenter. The cells may or may not be retained in the fermenter in this case. Another option is to remove the phenol from the fermentation broth while the fermenter broth remains in the fermenter.

DESCRIPTION

The invention relates to a method for whole cell biosynthesis of phenol from biomass as the starting material. Typically a source containing a significant proportion of fermentable sugars can be used in the method according to the invention. These sugars can include polysaccharides such as di-saccharides, e.g. saccharose, or tri-saccharides, e.g. kestose, as well as C-6 monosaccharides such as glucose, fructose or mannose and C-5 monosaccharides such as xylose and arabinose. A microbial strain, preferably a bacterial strain or a yeast strain, that is capable of converting sugar to phenol would enable the production of phenol from a wide range of renewable resources including sugar beet and sugar cane, starch-containing plants such as corn, wheat and rye, as well as lignocellulose e.g. from straw, wood or bagasse.

Given the major disadvantages of the above methods known in the art that usually are less efficient in energetic terms and also more complex with regard to the synthesis of phenol, there has been a need in the art for an improved method for producing phenol. It has therefore been the problem of the invention to provide a method for producing phenol from renewable sources that avoids the disadvantages of methods known in the art that are less efficient in energetic terms and more complex with regard to the synthesis of phenol.

The invention has solved said problem by providing a method of generating a recombinant host strain for producing phenol as described herein. The invention has further solved said problem by providing a recombinant host strain capable of producing phenol as described herein. The invention has further solved said problem by providing a method of producing phenol in the recombinant host strain. The invention has further solved said problem by providing a method and associated recombinant strain comprising an oxygen-tolerant hydroxybenzoate decarboxylase that is not sensitive to oxygen and is fully active at normal redox conditions, thus allowing phenol production at aerobic conditions. The invention has further solved said problem by providing a host strain that is resistant to phenol, thus allowing combined growth and phenol production at phenol concentrations high enough to enable production by continuous fermentation with the option of in-situ product recovery.

In particular, the invention has solved said problem by providing a method of generating a recombinant host strain for producing phenol, comprising the steps of:

a) providing a host comprising chorismate (CHO),

b) transforming said host with a first nucleic acid sequence comprising ubiC (SEQ ID NO: 1) encoding chorismate lyase, and

c) transforming said first transformant with a second nucleic acid sequence encoding an oxygen-tolerant 4-hydroxybenzoate decarboxylase, thereby generating a recombinant host that is capable of producing phenol under aerobic conditions,

wherein step b) and step c) are carried out simultaneously or sequentially.

Step a) of the method can make use of chorismate (CHO) that is present in the host. Chorismate is a key intermediate in the implemented pathway (see FIG. 1 and FIG. 2). It is a shared precursor for all three aromatic amino acids and is therefore naturally present in all organisms capable of producing aromatic amino acids, which includes all common microorganisms. Intracellular chorismate can therefore be produced from all fermentable sugars.

Step b) of the method provides the host with a first nucleic acid sequence, preferably a gene, the product of which converts chorismate (CHO) to 4-hydroxybenzoate (4-HB). ubiC (SEQ ID NO: 1) encodes the enzyme chorismate lyase that converts chorismate to 4-hydroxybenzoate (4-HB), thereby generating a recombinant host that overexpresses chorismate lyase (see FIG. 2 and FIG. 3). Thus, in a preferred embodiment of the invention, the first nucleic acid sequence is SEQ ID NO: 1.

Step c) of the method according to the invention additionally provides the host with a second nucleic acid sequence, preferably a gene cluster, the product of which converts 4-hydroxybenzoate (4-HB) to phenol, by introducing a nucleic acid into the host encoding an oxygen-tolerant 4-hydroxybenzoate decarboxylase (see e.g. FIG. 2 and FIG. 3). Said nucleic acid in step b) can comprise the gene cluster hbdBCD (SEQ ID NO 2) that expresses 4-hydroxybenzoate decarboxylase. The gene cluster hbdBCD of step c) can be derived from the E. coli strain E. coli O111:B4.

Thus, in a further embodiment of the method according to the invention, said second nucleic acid sequence comprises the gene cluster hbdBCD, as defined in SEQ ID NO 2. The enzyme encoded by SEQ ID NO: 2 is a 4-hydroxybenzoate decarboxylase that is oxygen-tolerant. Thus, in a preferred embodiment of the invention, said second nucleic acid sequence is SEQ ID NO: 2.

Thus, the invention has solved the above problem by providing a method of generating a recombinant host strain for producing phenol, comprising the steps of:

a) providing a host comprising chorismate (CHO),

b) transforming said host with a first nucleic acid sequence comprising ubiC (SEQ ID NO: 1) encoding chorismate lyase that converts chorismate (CHO) to 4-hydroxybenzoate (4-HB), and

c) transforming said first transformant with a second nucleic acid sequence encoding an oxygen-tolerant 4-hydroxybenzoate decarboxylase that converts 4-hydroxybenzoate (4-HB) to phenol, thereby generating a recombinant host that is capable of producing phenol under aerobic conditions,
wherein step b) and step c) are carried out simultaneously or sequentially.

In a preferred embodiment of the invention, said first nucleic acid sequence is SEQ ID NO: 1. In a further embodiment of the method according to the invention, said second nucleic acid sequence comprises the gene cluster hbdBCD, as defined in SEQ ID NO 2. The enzyme encoded by SEQ ID NO: 2 is a 4-hydroxybenzoate decarboxylase that is oxygen-tolerant. This, in a preferred embodiment of the invention, said second nucleic acid sequence is SEQ ID NO: 2.

Thus, the minimum requirements for producing phenol in a recombinant host according to the invention are the presence of chorismate in the host and the first nucleic acid sequence comprising ubiC (SEQ ID NO: 1) and the second nucleic acid sequence encoding an oxygen-tolerant 4-hydroxybenzoate decarboxylase that preferably is hbdBCD, as defined in SEQ ID NO: 2. The chorismate present in the host can be the endogenous chorismate that is produced naturally by the host, or it can be chorismate that is overproduced by the host, if said host comprises one or more genetic modifications to overproduce chorismate.

The first and second nucleic acid sequences transformed into the host in steps b) and c) can be on the same plasmid, on different plasmids or on the chromosome (chromosomal integration, e.g. Example 5). If the first and second nucleic acid sequences transformed into the host are on the same plasmid then step b) and step c) of the method can be carried out simultaneously (e.g. see Example 1). If the first and second nucleic acid sequences transformed into the host are on different plasmids then step b) and step c) of the method can be carried out sequentially. For example, the gene ubiC (SEQ ID NO: 1) can be transformed on a first plasmid into the host, and the gene cluster hbdBCD (SEQ ID NO: 2) can be transformed on a second plasmid into the host (see e.g. Example 3). In one embodiment, the host strain is transformed with ubiC and hbdBCD that are present on the same plasmid (e.g. see Example 1, pJF119ubiChbdBCD). In another embodiment, the host strain is transformed with ubiC (SEQ ID NO: 1) on the first plasmid pJF119 and with hbdBCD (SEQ ID NO: 2) on the second plasmid pACYC (e.g. see Example 3).

The technical advantage of the method of the invention over the prior art methods described above is that the economic feasibility of phenol production in a large scale production facility is improved. The invention allows a one-step conversion of sugar into phenol in a single vessel using continuous fermentation with in-situ product removal at aerobic conditions. This improves the sugar yield and the space time yield significantly. Compared to a fed-batch fermentation a continuous fermentation has a much better overall sugar yield since less sugar is needed to generate biomass which in case of a fed-batch fermentation needs to be generated for every new batch. The overall space-time yield is improved since no time is lost between the production phases as would be the case in a fed-batch fermentation (e.g. for harvesting the product, cleaning and sterilizing the fermenter, generating the biomass). Furthermore, the one-step conversion allows production using only one fermentation vessel. That reduces the complexity of the process and the capital expenditure for the production facility.

Compared to the synthesis pathway over tyrosine reported by Wierckx et al., the implemented synthesis pathway is less complex, more energy efficient and avoids large intracellular concentrations of tyrosine which would inhibit the biosynthesis pathway to phenol. As a result the method according to the invention is much more efficient, since it is able to achieve a better sugar yield (due to the energy efficiency) and a better space-time-yield (due to the shorter pathway and the avoidance of tyrosine as an intermediate), as compared to the methods known in the art.

In a further embodiment of the method according to the invention the host of step a) can overproduce chorismate (CHO). Such overproduction of chorismate in the host can be achieved by introducing one or more genetic modifications in the host. Accordingly, in a further embodiment of the method of the invention, the host can comprise one or more genetic modifications to overproduce chorismate. These genetic modifications have the effect that the host is producing chorismate at levels that are elevated, above the normal, endogenous physiological levels. Since more substrate is provided for the subsequent reactions in step b) (chorismate, CHO, to 4-hydroxybenzoate, 4-HB, by the ubiC gene product) and in step c) (4-HB to phenol by the hbdBCD gene product), more end product, i.e. phenol, is produced.

Such one or more genetic modifications can comprise a deletion of one or more of tyrR, pheA and tyrA that can be introduced into the host.

The TyrR protein, encoded by the gene tyrR, represses the expression of several of the genes in the common part of the aromatic amino acid pathway by binding to recognition sequences referred to as TyrR boxes. The TyrR protein is modulated by the presence of aromatic amino acids. In particular, the presence of tyrosine and ATP allows it to self-associate into a hexamer which can also bind to weak TyrR boxes some of which overlap the promotors of the genes in the aromatic amino acid pathway. In some cases the mechanism of repression involves exclusion of the RNA polymerase from the promotors, while in others it interferes with the ability of bound RNA polymerase to form open complexes or to exit the promotors. By deleting tyrR the regulatory effects caused by TyrR can be avoided completely, as shown in FIG. 2. The deletion of tyrR can be achieved by using the λ red recombinase according to the protocol by Datsenko and Wanner, as described in Example 1. Here, tyrR can be deleted by using the tyrR::FRT-kan cassette that is shown in SEQ ID NO:3, and as described in Example 1.

The gene pheA encodes for a bifunctional enzyme which catalyses the conversion of chorismate to prephenate (chorismate mutase) as well as the conversion of prephenate to keto-phenylpyruvate. The gene tyrA also encodes for a bifunctional enzyme which also catalyses the conversion of chorismate to prephenate (chorismate mutase) as well as the conversion of prephenate to 4-hydroxyphenylpyruvate (prephenate dehydrogenase). By deleting both the pheA and the tyrA gene the pathway from chorismate to phenylalanine and tyrosine can be completely inactivated since all chorismate activity is removed as well as the prephenate dehydratase and the prephenate dehydrogenase activity, as shown in FIG. 2. Deletion of pheA and tyrA can be achieved by using the pheAtyrA::FRT-CAT cassette that is shown in SEQ ID NO:4, as also described in Example 1.

In further embodiments of the invention, one, two or all three of tyrR, pheA and tyrA can be deleted in the host strain used. In a preferred embodiment of the invention, all three of the genes tyrR, pheA and tyrA are deleted in the host (ΔtyrRpheAtyrA), so that chorismate is overproduced. One example of such a recombinant strain carrying all three deletions is E. coli BW25113 ΔtyrRpheAtyrA that is listed in Table 1. The generation of the strain E. coli BW25113 ΔtyrR ΔpheAtyrA is described in Example 1.

In a further embodiment of the method said one or more genetic modifications to overproduce chorismate can comprise a transformation with one or more of aroG (SEQ ID NO: 9), aroG^fbr(SEQ ID NO: 10), aroB (SEQ ID NO: 11) and aroL (SEQ ID NO: 12). The host can be transformed individually with each one of aroG (SEQ ID NO: 9), aroG^fbr(SEQ ID NO: 10), aroB (SEQ ID NO: 11) and aroL (SEQ ID NO: 12). The host can also be transformed with each combination of aroG (SEQ ID NO: 9), aroG^fbr(SEQ ID NO: 10), aroB (SEQ ID NO: 11) and aroL (SEQ ID NO: 12) so that an optimal overproduction of chorismate is achieved.

The reactions catalysed by the gene products of aroG (SEQ ID NO: 9), aroG^fbr(SEQ ID NO: 10), aroB (SEQ ID NO: 11) and aroL (SEQ ID NO: 12) are depicted in FIG. 2. They all result in an overproduction of chorismate in the host.

The gene product of aroG (SEQ ID NO: 9) catalyses the reaction from E4P to DAHP, as shown in FIG. 2.

aroG^fbr(SEQ ID NO: 10) encodes for the same enzyme, except for a G to A mutation which makes the enzyme resistant to feedback inhibition, as reported by Kikuchi et al (Kikuchi, Y., Tsujimoto, K., Kurahashi, O. (1997) Applied and Environmental Microbiology 63 761-762) and shown in FIG. 6.

The gene product of aroB (SEQ ID NO: 11) catalyses the reaction from DAHP to 3DQ, as shown in FIG. 2.

The gene product of aroL (SEQ ID NO: 12) catalyses the reaction from SHI to SHI3P, as shown in FIG. 2.

The transformation of one or more of these genes results in an overproduction of chorismate in the host. Thus, in one embodiment of the method of the invention the host can comprise one or more genetic modifications to overproduce chorismate, wherein said one or more genetic modifications can be a transformation with one or more of aroG (SEQ ID NO: 9), aroG^fbr(SEQ ID NO: 10), aroB (SEQ ID NO: 11) and aroL (SEQ ID NO: 12).

The transformation of the host with one or more of aroG (SEQ ID NO: 9), aroG^fbr(SEQ ID NO: 10), aroB (SEQ ID NO: 11) and aroL (SEQ ID NO: 12) can be done as a single transformation step, wherein the genes that are transformed into the host are on the same plasmid. However, these transformations can also be performed in such a way that the genes that are introduced into the host are on separate plasmids or integrated directly on the chromosome.

In a further embodiment of the method said one or more genetic modifications that can be present in the host can comprise a deletion of one or more of tyrR, pheA and tyrA and can further comprise a transformation with one or more of aroG (SEQ ID NO: 9), aroG^fbr(SEQ ID NO: 10), aroB (SEQ ID NO: 11) and aroL (SEQ ID NO: 12).

In a particularly preferred embodiment of the method, the host of step a) is subjected to deleting all three of the genes tyrR, pheA and tyrA thereby generating the host ΔtyrRpheAtyrA, preferably E. coli BW25113 ΔtyrRpheAtyrA that is listed in Table 1 and described in Example 1, so that chorismate is overproduced. The host ΔtyrRpheAtyrA can subsequently be transformed with ubiC (SEQ ID NO: 1) in step b) and with hbdBCD (SEQ ID NO: 2) in step c), simultaneously or sequentially, thereby generating a host ΔtyrRpheAtyrA transformed with ubiC and hbdBCD. One example of such a strain is E. coli BW25113 ΔtyrRpheAtyrA transformed with ubiC and hbdBCD, as listed in Table 1, and as further described in Example 1 (E. coli BW25113 ΔtyrR ΔpheAtyrA).

In a further particularly preferred embodiment of the method, the host of step a) can be subjected to deleting all three of the genes tyrR, pheA and tyrA, thereby generating the host ΔtyrRpheAtyrA, so that chorismate is overproduced, which is then transformed with aroL (SEQ ID NO:12) and with ubiC (SEQ ID NO: 1) in step b) and with hbdBCD (SEQ ID NO: 2) in step c) of the method according to the invention, thereby generating a host ΔtyrRpheAtyrA transformed with aroL, ubiC and hbdBCD. One example of such a strain is E. coli BW25113 ΔtyrRpheAtyrA transformed with aroL, ubiC and hbdBCD, as listed in Table 1, and as further described in Example 2.

In a particularly preferred embodiment, the genetic modification to overproduce chorismate comprises a transformation with aroG^fbr(SEQ ID NO: 10), aroB (SEQ ID NO: 11), aroL (SEQ ID NO: 12), ubiC (SEQ ID NO: 1) and hbdBCD (SEQ ID NO: 2). Thus, one particularly preferred embodiment of the method according to the invention can generate the recombinant strain ΔtyrR ΔpheAtyrA transformed with aroG^fbr(SEQ ID NO: 10), aroB (SEQ ID NO: 11), aroL (SEQ ID NO: 12) and ubiC (SEQ ID NO: 1) and hbdBCD (SEQ ID NO: 2).

In another particularly preferred embodiment, the genetic modification to overproduce chorismate comprises a transformation with aroG^fbr(SEQ ID NO: 10), ubiC (SEQ ID NO: 1) and hbdBCD (SEQ ID NO: 2). Thus, one particularly preferred embodiment of the method according to the invention can generate the recombinant strain ΔtyrR ΔpheAtyrA transformed with aroG^fbr(SEQ ID NO: 10) and ubiC (SEQ ID NO: 1) and hbdBCD (SEQ ID NO: 2).

In another particularly preferred embodiment, the genetic modification to overproduce chorismate comprises a transformation with aroG^fbr(SEQ ID NO: 10), aroL (SEQ ID NO: 12), ubiC (SEQ ID NO: 1) and hbdBCD (SEQ ID NO: 2). Thus, one particularly preferred embodiment of the method according to the invention can generate the recombinant strain ΔtyrR ΔpheAtyrA transformed with aroG^fbr(SEQ ID NO: 10), aroL (SEQ ID NO: 12) and ubiC (SEQ ID NO: 1) and hbdBCD (SEQ ID NO: 2).

The host that can be used for the method according to the invention can be selected from the group consisting of bacteria, yeast and fungi. In a preferred embodiment, the bacterium is an Escherichia coli strain. The Escherichia coli strain can be selected from the group consisting of E. coli BW25113, E. coli DH10b, and E. coli LJ110. In a particularly preferred embodiment of the method according to the invention, E. coli BW25113 ΔtyrRpheAtyrA is used, as listed in Table 1 and as described in Example 1.

In a further embodiment of the method according to the invention the host can be a phenol-resistant host, preferably a phenol-resistant bacterium, more preferably a phenol-resistant Pseudomonas putida strain, more preferably Pseudomonas putida S12 and most preferably Pseudomonas putida S12 ΔpheApobA.

The transformation steps b) and c) that are performed in the method according to the invention can comprise plasmid transformation or chromosomal transformation. In plasmid transformation the transformed DNA is uncut and circular and therefore is held extrachromosomally in the host. In chromosomal transformation the transformed DNA is cut and therefore linear and can thus be integrated into the chromosomal genome of the host to be transformed.

The invention further provides a recombinant host strain obtainable by the method according to the invention, as described above.

In one embodiment, the recombinant host strain comprises chorismate and further comprises a first nucleic acid sequence comprising ubiC (SEQ ID NO: 1) and a second nucleic acid sequence encoding an oxygen-tolerant 4-hydroxybenzoate decarboxylase, wherein the recombinant strain is capable of producing phenol under aerobic conditions.

In a further embodiment of the host strain according to the invention said second nucleic acid sequence comprises hbdBCD, as defined in SEQ ID NO: 2.

In a further embodiment, the recombinant host strain can overproduce chorismate. Such overproduction of chorismate in the host can be achieved by introducing one or more genetic modifications in the host. Accordingly, in a further embodiment, the host strain can comprise one or more genetic modifications to overproduce chorismate. These genetic modifications have the effect that the host is producing chorismate at a higher rate than normal. Since substrate is provided at a higher rate for the subsequent reactions in step b) (chorismate, CHO, to 4-hydroxybenzoate, 4HB, by the ubiC gene product) and in step c) (4-hydroxybenzoate, 4HB, to phenol by the hbdBCD gene product) the end product, i.e. phenol, is produced at a higher rate.

In one embodiment, the recombinant host strain comprises one or more genetic modifications, wherein said genetic modification comprises a deletion of one or more of tyrR, pheA and tyrA. These genes and their gene products, as well as their deletion, have been described above.

In further embodiments of the invention, one, two or all three of tyrR, pheA and tyrA can be deleted in the recombinant host strain of the invention. In a preferred embodiment of the invention, all three of the genes tyrR, pheA and tyrA are deleted in the host, so that chorismate is overproduced (ΔtyrRpheAtyrA). One example of such a recombinant strain carrying all three deletions is E. coli BW25113 ΔtyrRpheAtyrA that is listed in Table 1, and as described in Example 1.

In a further embodiment, the recombinant host strain comprises one or more genetic modifications, wherein said genetic modification comprises a transformation with a nucleic acid sequence comprising one or more of aroG (SEQ ID NO: 9), aroG^fbr(SEQ ID NO: 10), aroB (SEQ ID NO: 11) and aroL (SEQ ID NO: 12). These genes and their gene products have been described above.

In a further embodiment, the recombinant host strain comprises one or more genetic modifications, wherein said genetic modification comprises a deletion of one or more of tyrR, pheA and tyrA; and further comprises a transformation with one or more of aroG (SEQ ID NO: 9), aroG^fbr(SEQ ID NO: 10), aroB (SEQ ID NO: 11) and aroL (SEQ ID NO: 12). These genes and their gene products have been described above.

In a particularly preferred embodiment of the recombinant host strain of the invention, the genetic modification to overproduce chorismate comprises a transformation with aroG (SEQ ID NO: 10), aroB (SEQ ID NO: 11), aroL (SEQ ID NO: 12), ubiC (SEQ ID NO: 1) and hbdBCD (SEQ ID NO: 2). Thus, one particularly preferred embodiment of the recombinant host strain according to the invention is the recombinant strain ΔtyrR ΔpheAtyrA transformed with aroG^fbr(SEQ ID NO: 10), aroB (SEQ ID NO: 11), aroL (SEQ ID NO: 12) and ubiC (SEQ ID NO: 1) and hbdBCD (SEQ ID NO: 2).

In another particularly preferred embodiment of the recombinant host strain of the invention, the genetic modification to overproduce chorismate comprises a transformation with aroG^fbr(SEQ ID NO: 10), aroL (SEQ ID NO: 12), ubiC (SEQ ID NO: 1) and hbdBCD (SEQ ID NO: 2). Thus, one particularly preferred embodiment of the recombinant host strain according to the invention is the recombinant strain ΔtyrR ΔpheAtyrA transformed with aroG^fbr(SEQ ID NO: 10), aroL (SEQ ID NO: 12) and ubiC (SEQ ID NO: 1) and hbdBCD (SEQ ID NO: 2).

In another particularly preferred embodiment of the recombinant host strain of the invention, the genetic modification to overproduce chorismate comprises a transformation with aroG^fbr(SEQ ID NO: 10), ubiC (SEQ ID NO: 1) and hbdBCD (SEQ ID NO: 2). Thus, one particularly preferred embodiment of the method according to the invention can generate the recombinant strain ΔtyrR ΔpheAtyrA transformed with aroG^fbr(SEQ ID NO: 10) and ubiC (SEQ ID NO: 1) and hbdBCD (SEQ ID NO: 2).

In a further embodiment, the recombinant host strain can be selected from the group consisting of bacteria, yeast and fungi. In a preferred embodiment, the bacterium is an Escherichia coli strain. In a further embodiment, said Escherichia coli strain can be selected from the group consisting of E. coli BW25113, E. coli DH10b, and E. coli LJ110. In a particularly preferred embodiment of the recombinant host strain according to the invention, E. coli BW25113 ΔtyrRpheAtyrA is used, as listed in Table 1, and as described in Example 1.

In a further embodiment of the recombinant strain according to the invention, said host can be a phenol-resistant host, preferably a phenol-resistant bacterium, more preferably a phenol-resistant Pseudomonas putida strain, more preferably Pseudomonas putida S12 and most preferably Pseudomonas putida S12 ΔpheApobA.

The deletion of pheA in Pseudomonas putida, as indicated by ΔpheA, inactivates the conversion of chorismate to prephenate (the chorismate mutase reaction, CHO to PREPH, see FIG. 2) thereby inactivating the pathway to phenylalanine and tyrosine. Unlike E. coli, Pseudomonas putida does not possess two isoenzymes for the chorismate mutase reaction, so it is sufficient to delete the pheA gene in Pseudomonas putida to inactivate the tyrosine and phenylalanine pathway. The gene pobA catalyses the conversion of 4-hydroxybenzoate to protocatechuate (4-hydroxybenzoate hydroxylase) which enables Pseudomonas putida to degrade 4-hydroxybenzoate. Deleting pheA and pobA, as indicated by ΔpheApobA, thus increases the availability of 4-hydroxybenzoate for phenol production, as the competing pathways are inactivated. E. coli does not have a hydroxybenzoate hydroxylase, so there is no corresponding deletion to be made if E. coli is used as the host.

The invention further provides a method of producing phenol in a recombinant host comprising the steps of

a) providing a recombinant host strain according to the invention, as described above, and

b) incubating said recombinant host strain under fermentation conditions thereby producing phenol.

In a further embodiment of the method according to the invention method, the phenol production can be induced. Such induction of phenol production can be in the absence or in the presence of oxygen (O₂). Phenol production can be induced by the presence or the absence of a specific chemical compound or by a change in a physical condition. For instance the presence of an inducer may activate the transcription of certain genes in the biosynthesis pathway to phenol (e.g. IPTG acting on the lac operon to express genes located on a plasmid), or the absence of, for instance, tyrosine may activate the expression of genes involved in the aromatic amino acid pathway from which phenol is derived. A change in a physical condition such as temperature, pH or O₂concentration may also activate the expression of genes involved in phenol synthesis.

In a further embodiment, the method of producing phenol in a recombinant strain can further comprise the step c) of harvesting the produced phenol from the recombinant host strain.

Step b) of the method of producing phenol in a recombinant host according to the invention can be performed as a batch fermentation, as a fed-batch fermentation or as a continuous fermentation.

In the context of the invention, batch fermentation refers to a fermentation method in which the complete fermentation medium is provided at the start of the fermentation. The product is harvested at the end of the fermentation (i.e. phenol).

In the context of the invention, fed-batch fermentation refers to a fermentation method in which a part of the fermentation medium is provided at the start of the fermentation, and a part is fed to the fermenter during the fermentation. The product is harvested at the end of the fermentation (i.e. phenol).

In the context of the invention, continuous fermentation refers to a fermentation method in which substrate is added and the product (i.e. phenol) is removed continuously during the fermentation.

In a further embodiment of the method of producing phenol in a recombinant strain, the fermentation conditions of step b) can comprise aerobic conditions. That means that both the reactions in the shake flasks as well as the fermenter can be performed under aerobic conditions. Such aerobic conditions can be implemented e.g. by gassing the shake flasks and/or fermenter with air.

In a further embodiment of the method of producing phenol in a recombinant strain, the fermentation conditions can comprise the presence of a raw sugar cane juice, wherein said raw sugar cane juice can preferably comprise a high concentration of 1-kestose. One example of this embodiment is shown in Example 6. Such sugar cane juice can be used as the substrate in such fermentation and can comprise, e.g glucose 14 g/l, fructose 24 g/l, sucrose 130 g/l, kestose 119 g/l and nystose 5 g/l, as measured by HPLC.

It will be apparent to those skilled in the art that various modifications can be made to the methods and recombinant host strains of the invention. Thus, it is intended that the present invention covers such modifications and variations, provided they come within the scope of the appended claims and their equivalents.

FIGURES, TABLES AND SEQUENCES

FIG. 1 shows the biosynthesis pathway from glucose to phenol.

E4P=erythrose-4-phosphate

DAHP=3-deoxy-D-arabino-heptulosonate-7-phosphate

3DQ=3-dehydroquinate

3DS=3-dehydroshikimate

SHI=shikimate

SHI3P=shikimate-3-phosphate

ESHI3P=5-enolpyruvyl-shikimate-3-phosphate

CHO=chorismate

4HB=4-hydroxybenzoate

PREPH=prephenate

FIG. 2 shows the metabolic engineering by the method of the invention of the cellular reaction network in a host in order to create a recombinant host strain according to the invention that overproduces phenol.

FIG. 3 shows the final two reactions in the phenol synthesis pathway that are catalysed by the ubiC (SEQ ID NO: 1) gene product (CHO to 4-HB) and by the hbdBCD (SEQ ID NO: 2) gene product hydroxybenzoic acid decarboxylase (4-HB to phenol).

FIG. 4 shows the HPLC analysis of the fermentation broth, as described in Example 1.

FIG. 5 shows the HPLC analysis of the fermentation broth, as described in Example 2.

FIG. 6 shows the genes aroG (SEQ ID NO: 9), aroG^fbr(SEQ ID NO: 10), aroB (SEQ ID NO: 11), aroL (SEQ ID NO: 12) and ubiC (SEQ ID NO: 1), which were all synthesised with restriction sites (underlined) for BglII and BamHI to allow integration into the plasmid. The ATG start codon and the TAA stop codon are in bold. The G to A feedback resistance mutation in aroG^fbr(SEQ ID NO: 10) is bold and underlined.

FIG. 7 shows the gene cluster hbdBCD (SEQ ID NO: 2), which was isolated from E. coli O111:B4 and integrated into the same plasmid that is already carrying ubiC by the appropriate restriction enzymes plasmid. The gene cluster has the composition hbdB: 0.6 kbp, hbdC: 1.4 kbp, hbdD: 0.2 kbp, as indicated.

FIG. 8 shows the HPLC analysis of the fermentation broth, as described in Example 3.

FIG. 9 shows the HPLC analysis of the fermentation broth, as described in Example 5.

FIG. 10 shows the HPLC analysis of the fermentation broth of shake flasks, as described in Example 6.

Table 1 shows a list of the E. coli strains, plasmids and genes used according to the invention.

Table 2 shows the results of Example 1 and Example 2.

SEQ ID NO: 1 shows the sequence of ubiC. The native gene ubiC, of which this sequence was derived, is found in the NCBI data base under the accession number CP000948, position 4350225 to 4350722. ubiC encodes chorismate lyase, which catalyses the reaction from chorismate (CHO) to 4-hydroxybenzoate (4-HB), as shown in FIG. 2 and in FIG. 3.

SEQ ID NO: 2 shows the sequence of the gene cluster hbdBCD derived from E. coli O111:B4. The gene cluster has the composition hbdB: 0.6 kbp, hbdC: 1.4 kbp, hbdD: 0.2 kbp, as depicted in FIG. 7. The sequence can be found in the NCBI data base under the accession number NC_013364 position 3434167 to 3431906. The gene cluster encodes 4-hydroxybenzoate decarboxylase that catalyses the reaction from 4-hydroxybenzoate (4-HB) to phenol, as shown in FIG. 2 and FIG. 3.

SEQ ID NO: 3 shows the sequence of the tyrR::FRT-kan cassette, which was used to delete tyrR.

SEQ ID NO: 4 shows the sequence of the pheAtyrA::FRT-CAT cassette, which was used to delete pheAtyrA.

SEQ ID NO: 5 shows the sequence of the knockout primer tyrR, the 5′ primer, which as used for deleting tyrR.

SEQ ID NO: 6 shows the sequence of the knockout primer tyrR, the 3′ primer, which as used for deleting tyrR.

SEQ ID NO: 7 shows the sequence of the knockout primer pheAtyrA, the 5′ primer, which as used for deleting pheAtyrA.

SEQ ID NO: 8 shows the sequence of the knockout primer pheAtyrA, the 3′ primer, which as used for deleting pheAtyrA.

SEQ ID NO: 9 shows the sequence of aroG. The native gene aroG, of which this sequence was derived, is found in the NCBI data base under the accession number CP000948, position 837448 to 838500. The aroG gene product which catalyses the reaction from E4P to DAHP, as shown in FIG. 2.

SEQ ID NO: 10 shows the sequence of aroG^fbr. The sequences as per SEQ ID NO: 7 differs from SEQ ID NO: 9 by the fact that G is changed to A at position 436, thereby generating the fbr (feedback resistance) mutant of aroG.

SEQ ID NO: 11 shows the sequence of aroB. The native gene aroB, of which this sequence was derived, is found in the NCBI data base under the accession number CP000948, position 3613165 to 3614253. The aroB gene product catalyses the reaction from DAHP to 3DQ, as shown in FIG. 2.

SEQ ID NO: 12 shows the sequence of aroL. The native gene aroL, of which this sequence was derived, is found in the NCBI data base under the accession number CP000948, position 344960 to 345484. The aroL gene product catalyses the reaction from SHI to SHI3P, as shown in FIG. 2.

SEQ ID NO: 13 shows the sequence of an insertion cassette with a Ptac promotor and a ribosome binding site upstream of the aroBaroG^fbrsequence, and a FRT flanked chloramphenicol resistance downstream of the aroBaroG^fbrsequence as well as a transcription terminator, as described in Example 5.

SEQ ID NO: 14 and SEQ ID NO: 15 show the sequences of the amplification primer pair that was used to amplify the insertion cassette, as shown in SEQ ID NO: 13.

SEQ ID NO: 16 shows the sequence of the cloning site on the chromosome after integration of the cassette in the fuc locus between the fucP and fucI genes, as described in Example 5. This sequence includes the chromosomal DNA sequences directly upstream and downstream of the cassette. The cassette is found between position 5148 and 9112 of SEQ ID NO: 16.

SEQ ID NO: 17 and SEQ ID NO: 18 show the sequence of the primer pair used for testing for successful chromosomal integration of the cassette, as described in Example 5. Mutants with defects in the fuc locus are not able to grow on L-fucose as a carbon source and will form pale colonies on MacConkey medium containing 1% fucose (contrary to wild type cells which will form red colonies, as described by Albermann et al. 2010). After selection on agar plates containing chloramphenicol, the positive colonies were further tested on MacConkey medium with 1% fucose. The fucose negative colonies were further tested with by PCR using primers SEQ ID NO: 17 for the 5′-test and SEQ ID NO 18 for the 3′-test.

EXAMPLES Example 1 Creating the Recombinant Strain E. coli BW25113 ΔtyrR ΔpheAtyrA pJF119ubiChbdBCD and Using it for Phenol Production by Fermentation

A novel biosynthesis pathway for synthesizing phenol from sugar via chorismate (CHO) was identified (see FIG. 1 and FIG. 2). This pathway was implemented in an E. coli strain and the further genetic modifications necessary to create a phenol producing strain were performed (see FIG. 2). In this way the whole cell biosynthesis of phenol was made possible. The created recombinant strain produced between 0.5 mM and 1.5 mM phenol in shake flask experiments and up to 5 mM in a 1 liter bioreactor fermentation. A list of the E. coli strains, plasmids and genes used is provided in Table 1.

The following genetic modifications were performed to overproduce chorismate in addition to the endogenous chorismate of the host strain E. coli BW25113: the genes pheA and tyrA were deleted in order to remove the chorismate mutase reaction that consumes chorismate so that chorismate is overproduced. These deletions make the strain auxotrophic towards phenylalanine and tyrosine. In addition, the regulatory gene tyrR that encodes an aporepressor for the expression of the Tyr regulon was deleted. The corepressor of tyrR is either tyrosine or phenylalanine plus tryptophan.

a. Creating the Host Strain E. coli BW25113 dtyrR dpheAtyrA

The knock out deletion of the genes pheA, tyrA and tyrR genes was performed by using recombination by the phage λ red recombinase according to the method of Datsenko and Wanner (Datsenko, K. A., Wanner, B. L., One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products (2000), PNAS, 97 6640-6645). pheA and tyrA are located right next to each other on the chromosome and were inactivated in one step. tyrR is located on a different place on the chromosome and was inactivated in a second step by the same method.

The insertion cassettes used for the disruptions contained an antibiotic resistance gene flanked by FRT (flippase recognition target) sites. Sequences homologous to regions adjacent to the gene to be inactivated were located at either end of the cassettes as described by Datsenko and Wanner. The insertion cassettes were amplified by PCR (polymerase chain reaction) from template plasmids with the antibiotic resistance gene and the FRT sites. The PCR primers contained the homologous regions and a priming site. The insertion cassette pheAtyrA::FRT-CAT used for pheAtyrA disruption had a chloramphenicol resistance and is given by SEQ ID NO: 4. The primers used for the amplification of the pheAtyrA knockout cassette (pheAtyrA::FRT-CAT cassette, SEQ ID NO: 4) are given by SEQ ID NO: 7 and SEQ ID NO: 8. The plasmid pCO1-FRT-CAT was used as template plasmid for the pheAtyrA::FRT-CAT cassette. The insertion cassette tyrR::FRT-kan used for tyrR disruption had a kanamycin resistance and is given by SEQ ID NO: 3. The primers used for the amplification of the tyrR knockout cassette (tyrR::FRT-kan, SEQ ID NO: 3) are given by SEQ ID NO: 5 and SEQ ID NO: 6. The plasmid pCO1-FRT-kan was used as template plasmid for the tyrR::FRT-kan cassette.

The tyrR::FRT-kan cassette was integrated into the chromosome of E. coli BW25113 by the λ red recombinase, thus yielding the strain E. coli BW25113 ΔtyrR. Cells in which the disruption had been successful were selected on agar plates containing kanamycin. Furthermore, control PCR was carried out to demonstrate the successful disruption. In the same way, the cassette pheAtyrA::FRT-CAT was integrated into the chromosome of E. coli BW25113 ΔtyrR by the λ red recombinase, thus yielding the strain E. coli BW25113 ΔtyrR ΔpheAtyrA (see Table 1). Cells in which the disruption had been successful were selected on agar plates containing chloramphenicol. Control PCR was again used to demonstrate the successful disruption of pheAtyrA. In addition, the phenylalanine and tyrosine auxotrophy of the created mutants was checked. The mutants were only able to grow in the presence of phenylalanine and tyrosine. In both chromosomal integrations the helper plasmid pKD46 was used to express the λ red recombinase. The antibiotic resistances were removed from E. coli BW25113 ΔtyrR ΔpheAtyrA by expressing a flippase using the helper plasmid pCP20.

b. Creating the Strain E. coli BW25113 dtyrR dpheAtyrA pJF119ubiChbdBCD

The plasmid pJF119 (Fürste, J. P., Pansegrau, W., Frank, R., Blocker, H., Scholz, P., Bagdasarian, M., Lanka, E. (1986) Molecular Cloning of the Plasmid RP4 Primase Region in a Multi-Host-Range tacP Expression Vector. Gene 48 119-131) was chosen as a vector for the over-expression of ubiC and hbdBCD.

The gene ubiC was designed with 5′ restriction sites for NdeI and BglII and 3′ restriction site for BamHI and synthesized by the company Geneart (part of Life Technologies). The delivery plasmid pMA was amplified in E. coli DH10b and the gene cut off by NdeI and BamHI restriction enzymes. Preparative agarose gel electrophoresis was used to purify the gene. A cloning site on pJF119 was opened by a sequential digest with first NdeI and then BamHI. The ubiC gene and the vector were ligated by T4 ligase (see FIG. 6 and SEQ ID NO: 1). The successful integration of the ubiC gene on the pJF119 plasmid was checked by digesting pJF119ubiC by NdeI/BamHI digestion and analyzing the DNA fragments by agarose gel electrophoresis. The protein expression profile was checked by expressing pJF119ubiC in E. coli DH10b and subsequent SDS-PAGE analysis of the cell extract. The activity of the gene product UbiC was demonstrated by incubating raw enzyme extracts of E. coli DH10b pJF119ubiC with chorismate and measuring the resulting 4-hydroxybenzoate production by HPLC. Finally, the plasmid pJF119ubiC was sequenced by the company Qiagen and the detected sequence was aligned to the original ubiC gene sequence and controlled for homology. All analyses confirmed the successful integration of ubiC into pJF119.

The gene cluster hbdBCD was amplified by PCR from the chromosome of the strain E. coli O111:B4 (ATCC 33780) using primers with restriction sites for HindIII/EcoRI. The primer product was then incorporated on the plasmid pUC19 by digesting pUC19 with HindIII/EcoRI and ligating the primer product with the opened pUC19 using T4 ligase (see FIG. 7 and SEQ ID NO: 2).

The plasmid pUC19hbdBCD was then digested with DrdI. The resulting DNA fragment of approx. 3 kb contained the hbdBCD gene cluster. This fragment was purified by preparative agarose gel electrophoresis. The fragment was incorporated into pJF119ubiC by digesting this vector with DrdI and ligating the fragment with the vector using T4 ligase. The correct cloning of hbdBCD was checked by digesting pJF119ubiChbdBCD with bglII and RsrII and separating the resulting fragments using agarose gel electrophoresis. The observed bands matched the expected DNA fragments. The activity of the gene product HbdBCD was demonstrated by incubating raw enzyme extracts of E. coli DH10b pJF119hbdBCD with 4-hydroxybenzoate and measuring the resulting phenol production by HPLC.

The pJF119 plasmid contains an ampicillin resistance which is used for selection. A second variant of the plasmid pJF119ubiChbdBCD was made by exchanging the ampicillin resistance for a kanamycin resistance. This was done by digesting pJF119hbdBCD with BspHI to remove the ampicillin resistance and then ligating the linear pJF119hbdBCD fragment with a gene for kanamycin resistance.

Finally, pJF119ubiChbdBCD was transferred into E. coli BW25113 ΔtyrR ΔpheAtyrA by electroporation to create the strain E. coli BW25113 ΔtyrR ΔpheAtyrA pJF119ubiChbdBCD (see Table 1). Both a variant with ampicillin resistance on the plasmid as well as a variant with kanamycine resistance on the plasmid was created.

c. Producing phenol from sugar with the strain E. coli BW25113 ΔtyrR ΔpheAtyrA pJF119ubiChbdBCD

E. coli BW25113 ΔtyrR ΔpheAtyrA pJF119ubiChbdBCD with ampicillin resistance was grown in a 10 ml shake flask culture and in a 1 1 bioreactor/fermenter, both under aerobic conditions. Such aerobic conditions were implemented by gassing the shake flask and/or bioreactor/fermenter with air.

The fermentation medium used for the shake flask culture was based on an E. coli medium published by Riesenberg et al (Riesenberg D., Schulz V., Knorre, W. A., Pohl, H-D., Korz, D., Sanders E. A., Ro, A., Deckwer, W-D. (1991) High cell density cultivation of Escherichia coli at controlled specific growth rate. Journal of Biotechnology 20 17-27). It contained the following compounds: 13.3 g/L KH₂PO₄, 4 g/L (NH₄)₂PO₄, 1.7 g/L Citrate, 2.5 g/l Luria Broth, 17.5 g/L Glucose, 0.024 g/L L-Phenylalanine, 0.016 g/L L-Tyrosine, 10 ml/l trace element solution, 0.6 g/L MgSO₄*7 H₂O, 0.2 mM CaCl₂*2 H₂O, 0.1 g/l ampicillin

The fermentation medium used in the bioreactor contained the following components: 15.5 g/L KH₂PO₄, 4.67 g/L (NH₄)₂PO₄, 1.98 g/L Citrate, 17.5 g/L Glucose, 0.5 g/L Thiamine, 0.037 g/L L-Phenylalanine, 0.024 g/L L-Tyrosine, 10 ml/l trace element solution, 0.6 g/L MgSO₄*7 H₂O, 0.2 mM CaCl₂*2 H₂O, 0.1 g/l ampicillin

The trace element solution had the following composition: 75 mg/L Fe(III)Citrat*H2O. 3.75 mg/L H₃BO₃, 18.75 mg/L Mn(II)Cl₂*4 H₂O, 10.5 mg/L EDTA (Titriplex III), 1.88 mg/L CuCl2*2 H₂O, 3.13 mg/L Na₂MoO₄*2 H₂O, 3.13 mg/L Co(II)Cl₂*6 H₂O, 10 mg/L Zn Acetate*2H₂O.

In the bioreactor the concentration of dissolved oxygen was controlled at pO₂=5% and the pH was controlled at pH=7.0 by addition of a 25% NH₄solution. That means that aerobic conditions were used, wherein the aerobic conditions were implemented e.g. by gassing the shake flasks and/or fermenter/bioreactor with air.

The expression of the genes on pJF119 was induced by adding IPTG to the culture once the bacteria had reached their exponential growth phase.

As a negative control shake flask fermentations were performed with the strains E. coli BW25113 ΔtyrR ΔpheAtyrA pJF119Δ and E. coli BW25113 ΔtyrR ΔpheAtyrA pUC19hbdBCD. pJF119Δ signifies a pJF119 plasmid without any added genes. The same shake flask fermentation medium was used for the negative controls and the fermentation procedure was identical including the addition IPTG.

The shake flask fermentation with E. coli BW25113 ΔtyrR ΔpheAtyrA pJF119ubiChbdBCD yielded 1.4 mM phenol after 24 hours. The fermentations in the bioreactor yielded 4.9 mM phenol after 40 hours. No phenol could be detected in the cultures of the negative controls (see Table 2). The concentrations were determined by HPLC-UV using a gradient method of 30 minutes and UV detection at 280 nm. The phenol peaks in the samples had identical retention times and UV-spectra to a phenol standard solution (see FIG. 4). HPLC-MS was used to detect the mass of phenol as a further confirmation of phenol production (see Table 2).

Example 2 Creating the Recombinant Strain E. coli BW25113 ΔtyrR ΔpheAtyrA pJF119aroLubiChbdBCD and Using it for Phenol Production by Fermentation

The host strain E. coli BW25113 ΔtyrR ΔpheAtyrA was developed as described in Example 1.

The gene aroL (SEQ ID NO: 12) was designed with a 5′ restriction sites for NdeI and BglII and 3′ restriction site for BamHI and synthesized by the company Geneart (part of Life Technologies), see also FIG. 6. It was then cloned in the plasmid pJF119 by the same method as described for the cloning of ubiC in Example 1 to create the plasmid pJF119aroL (see Table 1).

ubiC (SEQ ID NO: 1) was cloned onto the created plasmid pJF119aroL downstream of the aroL gene. pJF119aroL was digested with BamHI and ubiC was then cut off the delivery plasmid by digesting with BglII and BamHI. ubiC was ligated with the opened vector using T4 ligase to yield the plasmid pJF119aroLubiC. The correct integration of aroL and ubiC on pJF119 was checked by digesting with NdeI. This yielded two fragments; the aroL gene (0.5 kb) and the vector with ubiC (5.8 kb). A wrong orientation of ubiC would yield different fragments. One fragment would be the entire insert aroLubiC (1.0 kb) and the other the vector without insert (5.3 kb). The insert was also sequenced by Qiagen and the result aligned to the expected sequence. Both analyses confirmed the correct integration of aroL and ubiC in pJF119.

The hbdBCD gene cluster (SEQ ID NO: 2) was cloned on the pJF119aroLubiC plasmid by the method described in Example 1 and transformed into the strain E. coli BW25113 ΔtyrR ΔpheAtyrA to create E. coli BW25113 ΔtyrR ΔpheAtyrA pJF119aroLubiC (see Table 1).

The fermentation with E. coli BW25113 ΔtyrR ΔpheAtyrA pJF119aroLubiC was done in a shake flask using the same method and the same fermentation medium as described above in Example 1.

This shake flask fermentation yielded 0.59 mM phenol after 24 hours. No phenol could be detected in the cultures of the negative controls (see Table 2). The concentrations were determined by HPLC-UV using a gradient method of 30 minutes and UV detection at 280 nm. The phenol peaks in the samples had identical retention times and UV-spectra to a phenol standard solution (see FIG. 5). HPLC-MS was used to detect the mass of phenol as a further confirmation of phenol production (see Table 2).

Example 3 Creating the Recombinant Strain E. coli BW25113 ΔtyrR ΔpheAtyrA pJF119ubiC pACYChbdBCD and Using it for Phenol Production by Fermentation

The strain E. coli BW25113 ΔtyrR ΔpheAtyrA pJF119ubiC was created as described in Example 1.

The gene cluster hbdBCD was amplified by PCR from the chromosome of the strain E. coli O111:B4 (ATCC 33780) and cloned on plasmid pUC19 as described in Example 1. The plasmid pUC19hbdBCD was digested with EcoRI and HindIII to release the hbdBCD gene cluster. This DNA fragment was purified by preparative agarose gel electrophoresis. The plasmid pACYC was digested with EcoRI and HindIII. The linearized vector was purified by preparative agarose gel electrophoresis and ligated with the hbdBCD fragment. The resulting plasmid pACYC hbdBCD was transformed into E. coli DH10b and selected on agar plates containing chloramphenicol (pACYC contains a chloramphenicol resistance). The correct incorporation of hbdBCD on pACYC was controlled by digesting with EcoRI and HindIII and analysing the resulting fragments by agarose gel electrophoresis. This analysis confirmed the correct cloning of hbdBCD on pACYC. The plasmid pACYChbdBCD was transformed into the strain E. coli BW25113 ΔtyrR ΔpheAtyrA and a control digestion with EcoRI and HindIII was repeated with plasmid from the transformed strain. This analysis again confirmed the correct cloning of hbdBCD on pACYC. The plasmid pJF119ubiC, described in Example 1, was transformed into E. coli BW25113 ΔtyrR ΔpheAtyrA pACYChbdBCD to yield the strain E. coli BW25113 ΔtyrR ΔpheAtyrA pJF119ubiC pACYChbdBCD.

A fermentation with E. coli BW25113 ΔtyrR ΔpheAtyrA pJF119ubiC pACYChbdBCD was performed in a 1 liter bioreactor. The procedure and the fermentation medium was the same as described in Example 1 with the exception that the fermentation medium contained 0.1 g/l carbenicillin and 0.05 g/l chloramphenicol instead of ampicillin.

This bioreactor fermentation yielded 2.3 mM phenol after 90 hours. No phenol could be detected in the cultures of the negative controls (see Table 2). The concentrations were determined by HPLC-UV using a gradient method of 30 minutes and UV detection at 280 nm. The phenol peaks in the samples had identical retention times and UV-spectra to a phenol standard solution (see FIG. 8). HPLC-MS was used to detect the mass of phenol as a further confirmation of phenol production (see Table 2).

Example 4 Creating the Recombinant Strain E. coli BW25113 ΔtyrR ΔpheAtyrA pJF119hbdBCDubiC and Using it for Phenol Production by Fermentation

In Example 1 the hbdBCD gene cluster was located downstream of the ubiC gene and had its own lac promotor. The ubiC gene had a tac promotor. In this example the hbdBCD gene cluster was moved to a position just before the ubiC gene, right after its tac promotor so that both the hbdBCD and the ubiC gene were expressed by the tac promotor.

hbdBCD was cut from the pJF119ubiChbdBCD construct described in Example 1 with the restriction enzymes NdeI and HindIII and purified by preparative agarose gel electrophoresis. The pACYC plasmid was cut with the same restriction enzymes, dephosphorylated and ligated with the hbdBCD gene yielding the construct pACYChbdBCD.

The construct pACYChbdBCD was then digested with EcoRI to release the hbdBCD gene with EcoRI overhangs. The construct pJF119ubiC described in Example 1 was digested with EcoRI, dephosphorylated and ligated with the hbdBCD gene to yield the construct pJF119hbdBCDubiC. The expression of hbdBCD after induction with IPTG was demonstrated by agarose gel electrophoresis.

The plasmid construct pJF119hbdBCDubiC was transformed in the strain BW25113 ΔtyrR ΔpheAtyrA described in Example 1. A shake flask fermentation with IPTG induction performed according to the method described in Example 1 yielded 0.093 mM phenol.

Example 5 Creating the Recombinant Strain E. coli BW25113 ΔpheAtyrA ΔtyrR Fuc::P_tacaroBaroG^fbrpJF119ubiChbdBCD and Using it for Phenol Fermentation

The genes aroB (sequence number) and aroG^fbr(sequence number) were integrated on the chromosome of the strain E. coli BW25113 ΔpheAtyrA ΔtyrR using an insertion cassette with a Ptac promotor and a ribosome binding site upstream of the aroBaroG^fbrsequence, and a FRT flanked chloramphenicol resistance downstream of the aroBaroG^fbrsequence as well as a transcription terminator (chromosomal integration). The sequence for the insertion cassette is given by SEQ ID NO: 13. The sequence for the primers used to amplify the insertion cassette is given by SEQ ID NO: 14 (5′-TGC TGT GCT CAC TGT TTT TTC TTT GGG CGG TAG CCA ATA ACC TTA ACG ACA TTT TAT TA TCA AGG CGC ACT CCC GTT CTG G-3′) and SEQ ID NO: 15 (5′-CAG CAT GGA GGC GAG AGT GAT AAA GTC TGC GCC AAC GTG GCC GAT GGT CAG AAC CCC CAG GGT TAT TGT CTC ATG AGC G-3′). The phage λ red recombinase method was used to integrate the cassette as described in Example 1. The cassette was integrated in the fuc locus on the chromosome between the fucP and fucI genes and disrupted these. The sequence of the cloning site on the chromosome is given by SEQ ID NO 16. This sequence includes the chromosomal DNA sequences directly upstream and downstream of the cassette. The cassette is found between position 5148 and 9112.

Mutants with defects in the fuc locus are not able to grow on L-fucose as a carbon source and will form pale colonies on MacConkey medium containing 1% fucose (contrary to wild type cells which will form red colonies, as described by Albermann et al. 2010). After selection on agar plates containing chloramphenicol, the positive colonies were further tested on MacConkey medium with 1% fucose. The fucose negative colonies were further tested with by PCR using primers SEQ ID NO: 17 (GGC CTA TTT CCC TAA AGG GTT TAT TGA G) for the 5′-test and SEQ ID NO 18 (GACGATACACTTTGGTCTCTTCAACGTTG) for the 3′-test. The chloramphenicol resistance was removed by expressing a flippase as described in Example 1, thus creating the strain E. coli BW25113 ΔpheAtyrA ΔtyrR fuc::P_tacaroBaroG^fbr. Transformation of the plasmid construct pJF119ubiChbdBCD described in Example 1 then yielded the strain E. coli BW25113 ΔpheAtyrA ΔtyrR fuc::P_tacaroBaroG^fbrpJF119ubiChbdBCD. A shake flask fermentation with IPTG induction was performed as described in Example 1. A phenol concentration of 1.2 mM was measured by HPLC after 24 hours. The HPLC method described in Example 1 was used. The phenol peaks in the samples had identical retention times and UV-spectra to a phenol standard solution (see FIG. 9).

Example 6 Phenol Production by Fermentation Using a Raw Sugar Cane Juice Containing a High Proportion of Kestose

Fermentations with the strain E. coli BW25113 ΔtyrR ΔpheAtyrA pJF119ubiChbdBCD in shake flasks and in a bioreactor were performed using raw sugar cane juice as the sole energy and carbon source. The sugar cane juice was extracted from a transgenic sugar cane plant containing a high proportion of 1-kestose as well as sucrose, fructose, glucose and nystose. The concentrations of these sugars in the sugar cane juice had been measured by HPLC and had the following concentrations; glucose 14 g/l, fructose 24 g/l, sucrose 130 g/l, kestose 119 g/l, nystose 5 g/l. Further compounds in the sugar cane juice were not analysed. The juice was then used as energy and carbon source in the Riesenberg medium described in Example 1 instead of glucose. The sugar cane juice was added to yield a total sugar concentration of 15 g/l in the final medium. Thus the medium for the shake flask fermentation was given as follows; 13.3 g/L KH₂PO₄, 4 g/L (NH₄)₂PO₄, 1.7 g/L citrate, 2.5 g/l Luria Broth, 0.051 l/l sugar cane juice, 0.024 g/L L-phenylalanine, 0.016 g/L L-tyrosine, 10 ml/l trace element solution, 0.6 g/L MgSO₄*7 H₂O, 0.2 mM CaCl₂*2 H₂O, 0.1 g/l ampicillin. The medium used for fermentation in the bioreactor was given as follows; 15.5 g/L KH₂PO₄, 4.67 g/L (NH₄)₂PO₄, 1.98 g/L Citrate, 0.051 l/l sugar cane juice, 0.5 g/L Thiamine, 0.037 g/L L-Phenylalanine, 0.024 g/L L-Tyrosine, 10 ml/l trace element solution, 0.6 g/L MgSO₄*7 H₂O, 0.2 mM CaCl₂*2 H₂O, 0.1 g/l ampicillin. The trace element solution was defined in Example 1.

The fermentation in shake flasks yielded a phenol concentration of 3.1 mM after complete depletion of all sugars while the fermentation in the bioreactor yielded a phenol concentration of 0.9 mM after depletion of all sugars. These results demonstrate that it is possible to produce phenol from raw sugar juice containing a mixture of sugars including a high proportion of 1-kestose. The chromatograms of the phenol HPLC-measurement and the UV spectra of the fermentation in shake flask are given in FIG. 10.

TABLE 1

Strain	Plasmid	Gene	Resistance

E. coli BW25113	ΔtyrRpheAtyrA pJF119	aroB	amp, chromosomal kan + CAT
E. coli BW25113	ΔtyrRpheAtyrA pJF119	aroGfbr	amp chromosomal kan + CAT
E. coli BW25113	ΔtyrRpheAtyrA pJF119	aroL	amp, chromosomal kan + CAT
E. coli BW25113	ΔtyrRpheAtyrA pJF119	ubiC	amp, chromosomal kan + CAT
E. coli BW25113	ΔtyrRpheAtyrA pUC19	hbdBCD	amp, chromosomal kan + CAT
E. coli BW25113	ΔtyrRpheAtyrA pJF119	aroBaroL	amp, chromosomal kan + CAT
E. coli BW25113	ΔtyrRpheAtyrA pJF119	aroLaroB	amp, chromosomal kan + CAT
E. coli BW25113	ΔtyrRpheAtyrA pJF119	aroLubiC	amp, chromosomal kan + CAT
E. coli BW25113	ΔtyrRpheAtyrA pJF119	ubiCaroB	amp, chromosomal kan + CAT
E. coli BW25113	ΔtyrRpheAtyrA pJF119	ubiCaroL	amp, chromosomal kan + CAT
E. coli BW25113	ΔtyrRpheAtyrA pJF119	aroGfbr aroL	amp, chromosomal kan + CAT
E. coli BW25113	ΔtyrRpheAtyrA pJF119	aroGfbr ubiC	amp, chromosomal kan + CAT
E. coli BW25113	ΔtyrRpheAtyrA pJF119	aroLubiCaroB	amp, chromosomal kan + CAT
E. coli BW25113	ΔtyrRpheAtyrA pJF119	aroGfbr aroLaroB	amp, chromosomal kan + CAT
E. coli BW25113	ΔtyrRpheAtyrA pJF119	a roGfbr aroLubiC	amp, chromosomal kan + CAT
E. coli BW25113	ΔtyrRpheAtyrA pJF119	aroLubiCaroBaroGfbr	amp, chromosomal kan + CAT
E. coli BW25113	ΔtyrRpheAtyrA pJF119	ubiChbdBCD	amp, chromosomal kan + CAT or kan only
E. coli BW25113	ΔtyrRpheAtyrA pJF119	aroLubiChbdBCD	amp, chromosomal kan + CAT or kan only
E. coli BW25113	ΔtyrRpheAtyrA pJF119	aroLubiChbdBCD	amp, chromosomal kan + CAT or kan only
E. coli BW25113	ΔtyrRpheAtyrA pJF119	ubiCaroLhbdBCD	amp, chromosomal kan + CAT or kan only
E. coli BW25113	ΔtyrRpheAtyrA pJF119	ubiCaroLhbdBCD	amp, chromosomal kan + CAT or kan only
E. coli BW25113	ΔtyrRpheAtyrA pJF119	aroLubiCaroBhbdBCD	amp, chromosomal kan + CAT or kan only
E. coli BW25113	ΔtyrRpheAtyrA pACYC	hbdBCD	CAT
E. coli BW25113	ΔtyrRpheAtyrA pACYC /pJF119	pJF119ubiC, pACYChbdBCD	CAT
E. coli BW25113	ΔtyrRpheAtyrA pACYC /pJF119	pJF119aroLubiC, pACYChbdBCD	CAT
E. coli BW25113	ΔtyrRpheAtyrA pACYC /pJF119	pJF119ubiCaroL, pACYChbdBCD	CAT

E. coli BW25113	ΔtyrRpheAtyrA pJF119 aroLubiCaroBaroGfbr hbdBCD	amp, chromosomal kan + CAT

TABLE 2

		Conc. Phenol
		[mM]	Detection of
	Fermentation	measured by	phenol by
Strain	device	HPLC-UV	HPLC_MS	Experiment

E. coli BW25113	Shake flask	below	no	Example 1, 2,
ΔpheAtyrAΔtyrR		detection limit		3
pJF119Δ
E. coli BW25113	Shake flask	below	Not measured	Example 1, 2,
ΔpheAtyrAΔtyrR		detection limit		3
pUC19hbdBCD
E. coli BW25113	Shake flask	1.44	yes	Example 1
ΔpheAtyrAΔtyrR
pJF119ubiChbdBCD
E. coli BW25113	Fermenter	4.9	yes	Example 1
ΔpheAtyrAΔtyrR
pJF119ubiChbdBCD
E. coli BW25113	Shake flask	0.59	yes	Example 2
ΔpheAtyrAΔtyrR
pJF119aroLubiChbdBCD
E. coli BW25113	Fermenter	2.3	yes	Example 3
ΔpheAtyrAΔtyrR
pACYChbdBCD
pJF119ubiC
E. coli BW25113	Shake flask	0.093	Not measured	Example 4
ΔpheAtyrAΔtyrR
pJF1 l9hbdBCDubiC
E. coli BW25113	Shake flask	1.2	Not measured	Example 5
ΔpheAtyrAΔtyrR
fuc::P_tac-aroBaroG^fbr
pJF119ubiChbdBCD
E. coli BW25113	Shake flask	3.1	Not measured	Example 6
ΔpheAtyrAΔtyrR	with sugar cane
pACYChbdBCD	juice
pJF119ubiC
E. coli BW25113	Fermenter with	0.9	Not measured	Example 6
ΔpheAtyrAΔtyrR	sugar cane juice
pACYChbdBCD
pJF119ubiC

“No” signifies that the concentration is below 1 mg/l.
“Yes” signifies that the concentration is above 1 mg/l

Claims

The invention claimed is:

1. A method of generating a recombinant host strain for producing phenol, comprising the steps of

a) providing a host comprising chorismate,

c) transforming said host with a second nucleic acid sequence encoding an oxygen-tolerant 4-hydroxybenzoate decarboxylase, thereby generating a recombinant host that is capable of producing phenol under aerobic conditions,

wherein step b) and step c) are carried out simultaneously or sequentially.

2. The method according to claim 1, wherein said second nucleic acid sequence comprises hbdBCD (SEQ ID NO:2).

3. The method according to claim 1, wherein the host of step a) is overproducing chorismate, wherein said host optionally comprises one or more genetic modifications to overproduce chorismate.

4. The method according to claim 3, wherein said genetic modification comprises a deletion of one or more of tyrR, pheA and tyrA.

5. The method according to claim 3, wherein said genetic modification comprises a transformation with one or more of aroG (SEQ ID NO: 9), aroG^fbr(SEQ ID NO: 10), aroB (SEQ ID NO: 11) and aroL (SEQ ID NO: 12).

6. The method according to claim 3, wherein said genetic modification comprises a deletion of one or more of tyrR, pheA and tyrA; and further comprises

a transformation with one or more of aroG (SEQ ID NO: 9), aroG^fbr(SEQ ID NO: 10), aroB (SEQ ID NO: 11) and aroL (SEQ ID NO: 12).

7. The method according to claim 1, wherein said host is selected from the group consisting of bacteria, yeast and fungi.

8. The method according to claim 1, wherein said host is a phenol-resistant host.

9. The method of claim 1, wherein the transformation in steps b) and c) comprise plasmid transformation and/or chromosomal transformation.

10. A recombinant host strain obtainable by the method of claim 1.

11. A recombinant host strain comprising chorismate and further comprising a first nucleic acid sequence comprising ubiC (SEQ ID NO: 1) and a second nucleic acid sequence encoding an oxygen-tolerant 4-hydroxybenzoate decarboxylase, wherein the recombinant strain is capable of producing phenol under aerobic conditions.

12. The recombinant host strain of claim 11, wherein said second nucleic acid sequence comprises hbdBCD (SEQ ID NO: 2).

13. The recombinant host strain of claim 1, wherein said host strain is overproducing chorismate, wherein said host strain optionally comprises one or more genetic modifications to overproduce chorismate.

14. The recombinant host strain of claim 13, wherein said genetic modification comprises a transformation with one or more of aroG (SEQ ID NO: 9), aroG^fbr(SEQ ID NO: 10), aroB (SEQ ID NO: 11) and aroL (SEQ ID NO:12).

15. The recombinant strain of claim 13, wherein said genetic modification comprises a deletion of one or more of tyrR, pheA and tyrA; and further comprises

16. The recombinant strain of one or more of claim 13, wherein said host is selected from the group consisting of bacteria, yeast and fungi.

17. The recombinant strain of claim 13, wherein said host is a phenol-resistant host.

18. A method of producing phenol in a recombinant host comprising the steps of

a) providing a recombinant host strain according to claim 10, and

19. The method of claim 18, wherein phenol production is induced, and wherein the produced phenol optionally is harvested in a further step c) of harvesting the phenol from the recombinant host strain, and wherein optionally at least step b) is performed as a batch fermentation, as a fed-batch fermentation or as a continuous fermentation.

20. The method of claim 18, wherein said fermentation conditions comprise aerobic conditions.

21. The method of claim 18, wherein said fermentation conditions comprise the presence of a raw sugar cane juice, wherein said raw sugar cane juice optionally comprises a high concentration of 1-kestose.

22. A method of producing phenol in a recombinant host comprising the steps of

a) providing a recombinant host strain according to claim 11, and